The NSF-funded SoyMap II project, led by Scott Jackson, involved sequencing corresponding regions around six regions of interest from eight Glycine species, to gain insights into the polyploid and perennial genome evolution and genetic potential for soybean improvement. This project finished in 2012. See more information about the project, including pictures of the focal species and descriptions of the target regions, at legacy.soybase.org/soymap2.
A subsequent project, led by Jianxin Ma and Dajian Zhang, with funding primarily from the Shandong Province (China), completed the genome assemblies for the species used in the SoyMap II project. The Zhuang, Wang et al. (2022) paper below describes the genome assemblies and analyses from the second project. See references therein for further citations and descriptions of the species and objectives for both projects.
Citation: Zhuang Y, Wang X, Li X, Hu J, Fan L, Landis JB, Cannon SB, Grimwood J, Schmutz J, Jackson SA, Doyle JJ, Zhang XS, Zhang D, Ma J. Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. Nat Plants. 2022 Mar;8(3):233-244.
Polyploidy and life-strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and the genetic bases of such transitions remain elusive. We assembled chromosome-level genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes. These perennial diploids exhibit greater genome stability and possess fewer centromere repeats than the annuals. Biased subgenomic fractionation occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with pre-existing local subgenomic differentiation. Two genes annotated to modulate vegetative-reproductive phase transition and lateral shoot outgrowth were postulated as candidates underlying the perenniality-annuality transition. Our study provides insights into polyploid genome evolution and lays a foundation for unleashing genetic potential from the perennial gene pool for soybean improvement.